data_3S3R # _model_server_result.job_id Arqa01XxiwbdA6aWYf7rZg _model_server_result.datetime_utc '2024-12-26 19:58:13' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 3s3r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":324}' # _entry.id 3S3R # _exptl.entry_id 3S3R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 576.749 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description Nalpha-[(4-methylpiperazin-1-yl)carbonyl]-N-[(3S)-1-phenyl-5-(phenylsulfonyl)pentan-3-yl]-L-phenylalaninamide _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 3S3R _cell.length_a 77.633 _cell.length_b 103.121 _cell.length_c 100.697 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3S3R _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,G 1 1 B,E,H 2 1 C,F,I 3 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N ? 2 F N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 16 A CYS 85 1_555 A SG CYS 45 A CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 A SG CYS 28 A CYS 97 1_555 A SG CYS 72 A CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf3 A SG CYS 64 A CYS 133 1_555 A SG CYS 130 A CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf4 A SG CYS 65 A CYS 134 1_555 A SG CYS 68 A CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf5 A SG CYS 101 A CYS 170 1_555 A SG CYS 134 A CYS 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf6 A SG CYS 109 A CYS 178 1_555 A SG CYS 120 A CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf7 B SG CYS 16 B CYS 85 1_555 B SG CYS 45 B CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf8 B SG CYS 28 B CYS 97 1_555 B SG CYS 72 B CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf9 B SG CYS 64 B CYS 133 1_555 B SG CYS 130 B CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf10 B SG CYS 65 B CYS 134 1_555 B SG CYS 68 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf11 B SG CYS 101 B CYS 170 1_555 B SG CYS 134 B CYS 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf12 B SG CYS 109 B CYS 178 1_555 B SG CYS 120 B CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf13 C SG CYS 16 C CYS 85 1_555 C SG CYS 45 C CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf14 C SG CYS 28 C CYS 97 1_555 C SG CYS 72 C CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf15 C SG CYS 64 C CYS 133 1_555 C SG CYS 130 C CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf16 C SG CYS 65 C CYS 134 1_555 C SG CYS 68 C CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf17 C SG CYS 101 C CYS 170 1_555 C SG CYS 134 C CYS 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? disulf ? disulf18 C SG CYS 109 C CYS 178 1_555 C SG CYS 120 C CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? covale ? covale1 A SG CYS 31 A CYS 100 1_555 D C21 0IW . A 0IW 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? covale ? covale2 B SG CYS 31 B CYS 100 1_555 E C21 0IW . B 0IW 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? covale ? covale3 C SG CYS 31 C CYS 100 1_555 F C21 0IW . C 0IW 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? # _chem_comp.formula 'C32 H40 N4 O4 S' _chem_comp.formula_weight 576.749 _chem_comp.id 0IW _chem_comp.mon_nstd_flag . _chem_comp.name Nalpha-[(4-methylpiperazin-1-yl)carbonyl]-N-[(3S)-1-phenyl-5-(phenylsulfonyl)pentan-3-yl]-L-phenylalaninamide _chem_comp.type peptide-like _chem_comp.pdbx_synonyms 'APC-3316, bound form;4-Methylpiperazine-1-carboxylic acid [1-[(3-benzenesulfonyl-1-phenethylallyl)carbamoyl]-2-phenylethyl]amide, bound form' # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag N1 C 0IW sing 1 n n N1 C2 0IW sing 2 n n N1 C6 0IW sing 3 n n C O 0IW doub 4 n n C N 0IW sing 5 n n C2 C3 0IW sing 6 n n C3 N4 0IW sing 7 n n N4 CM 0IW sing 8 n n N4 C5 0IW sing 9 n n C5 C6 0IW sing 10 n n N CA 0IW sing 11 n n CA C1 0IW sing 12 n n CA CB 0IW sing 13 n n C1 O1 0IW doub 14 n n C1 N2 0IW sing 15 n n CB CG 0IW sing 16 n n CG CD1 0IW doub 17 n y CG CD2 0IW sing 18 n y CD1 CE1 0IW sing 19 n y CD2 CE2 0IW doub 20 n y CE1 CZ 0IW doub 21 n y CE2 CZ 0IW sing 22 n y C11 C21 0IW sing 23 n n C11 S1 0IW sing 24 n n C21 C31 0IW sing 25 n n C31 N2 0IW sing 26 n n C31 C4 0IW sing 27 n n C4 C51 0IW sing 28 n n C51 C1' 0IW sing 29 n n C1' C2' 0IW doub 30 n y C1' C6' 0IW sing 31 n y C2' C3' 0IW sing 32 n y C3' C4' 0IW doub 33 n y C4' C5' 0IW sing 34 n y C5' C6' 0IW doub 35 n y C12 C22 0IW doub 36 n y C12 C61 0IW sing 37 n y C22 C32 0IW sing 38 n y C32 C41 0IW doub 39 n y C41 S1 0IW sing 40 n n C41 C52 0IW sing 41 n y S1 O11 0IW doub 42 n n S1 O2 0IW doub 43 n n C52 C61 0IW doub 44 n y C2 H21 0IW sing 45 n n C2 H22 0IW sing 46 n n C3 H31 0IW sing 47 n n C3 H32 0IW sing 48 n n CM HM1 0IW sing 49 n n CM HM2 0IW sing 50 n n CM HM3 0IW sing 51 n n C5 H51 0IW sing 52 n n C5 H52 0IW sing 53 n n C6 H61 0IW sing 54 n n C6 H62 0IW sing 55 n n N H 0IW sing 56 n n CA HA 0IW sing 57 n n CB HB2 0IW sing 58 n n CB HB3 0IW sing 59 n n CD1 HD1 0IW sing 60 n n CD2 HD2 0IW sing 61 n n CE1 HE1 0IW sing 62 n n CE2 HE2 0IW sing 63 n n CZ HZ 0IW sing 64 n n C11 H11 0IW sing 65 n n C11 H221 0IW sing 66 n n C21 H211 0IW sing 67 n n C21 H24 0IW sing 68 n n C31 H3 0IW sing 69 n n N2 HN2 0IW sing 70 n n C4 H41 0IW sing 71 n n C4 H42 0IW sing 72 n n C51 H511 0IW sing 73 n n C51 H521 0IW sing 74 n n C2' H2' 0IW sing 75 n n C3' H3' 0IW sing 76 n n C4' H4' 0IW sing 77 n n C5' H5' 0IW sing 78 n n C6' H6' 0IW sing 79 n n C12 H1 0IW sing 80 n n C22 H2 0IW sing 81 n n C32 H33 0IW sing 82 n n C52 H5 0IW sing 83 n n C61 H6 0IW sing 84 n n # _atom_sites.entry_id 3S3R _atom_sites.fract_transf_matrix[1][1] 0.012881 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009697 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.009931 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code D 2 0IW A 1 324 300 0IW 0IW . E 2 0IW B 1 324 300 0IW 0IW . F 2 0IW C 1 324 300 0IW 0IW . G 3 HOH A 1 1 1 HOH HOH . G 3 HOH A 2 2 2 HOH HOH . G 3 HOH A 3 3 3 HOH HOH . G 3 HOH A 4 8 8 HOH HOH . G 3 HOH A 5 9 9 HOH HOH . G 3 HOH A 6 12 12 HOH HOH . G 3 HOH A 7 15 15 HOH HOH . G 3 HOH A 8 19 19 HOH HOH . G 3 HOH A 9 20 20 HOH HOH . G 3 HOH A 10 21 21 HOH HOH . G 3 HOH A 11 22 22 HOH HOH . G 3 HOH A 12 23 23 HOH HOH . G 3 HOH A 13 24 24 HOH HOH . G 3 HOH A 14 25 25 HOH HOH . G 3 HOH A 15 26 26 HOH HOH . G 3 HOH A 16 33 33 HOH HOH . G 3 HOH A 17 34 34 HOH HOH . G 3 HOH A 18 39 39 HOH HOH . G 3 HOH A 19 45 45 HOH HOH . G 3 HOH A 20 46 46 HOH HOH . G 3 HOH A 21 52 52 HOH HOH . G 3 HOH A 22 53 53 HOH HOH . G 3 HOH A 23 54 54 HOH HOH . G 3 HOH A 24 55 55 HOH HOH . G 3 HOH A 25 56 56 HOH HOH . G 3 HOH A 26 58 58 HOH HOH . G 3 HOH A 27 64 64 HOH HOH . G 3 HOH A 28 66 66 HOH HOH . H 3 HOH B 1 5 5 HOH HOH . H 3 HOH B 2 7 7 HOH HOH . H 3 HOH B 3 10 10 HOH HOH . H 3 HOH B 4 13 13 HOH HOH . H 3 HOH B 5 17 17 HOH HOH . H 3 HOH B 6 18 18 HOH HOH . H 3 HOH B 7 27 27 HOH HOH . H 3 HOH B 8 29 29 HOH HOH . H 3 HOH B 9 30 30 HOH HOH . H 3 HOH B 10 31 31 HOH HOH . H 3 HOH B 11 32 32 HOH HOH . H 3 HOH B 12 36 36 HOH HOH . H 3 HOH B 13 38 38 HOH HOH . H 3 HOH B 14 40 40 HOH HOH . H 3 HOH B 15 41 41 HOH HOH . H 3 HOH B 16 42 42 HOH HOH . H 3 HOH B 17 43 43 HOH HOH . H 3 HOH B 18 44 44 HOH HOH . H 3 HOH B 19 49 49 HOH HOH . H 3 HOH B 20 51 51 HOH HOH . H 3 HOH B 21 57 57 HOH HOH . H 3 HOH B 22 59 59 HOH HOH . H 3 HOH B 23 61 61 HOH HOH . H 3 HOH B 24 62 62 HOH HOH . H 3 HOH B 25 63 63 HOH HOH . I 3 HOH C 1 4 4 HOH HOH . I 3 HOH C 2 6 6 HOH HOH . I 3 HOH C 3 11 11 HOH HOH . I 3 HOH C 4 14 14 HOH HOH . I 3 HOH C 5 16 16 HOH HOH . I 3 HOH C 6 28 28 HOH HOH . I 3 HOH C 7 35 35 HOH HOH . I 3 HOH C 8 37 37 HOH HOH . I 3 HOH C 9 47 47 HOH HOH . I 3 HOH C 10 48 48 HOH HOH . I 3 HOH C 11 50 50 HOH HOH . I 3 HOH C 12 60 60 HOH HOH . I 3 HOH C 13 65 65 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 N N1 0IW . . . D 2 0.836 -14.511 -22.702 1 41.84 ? N1 0IW 324 A 1 HETATM 2 C C 0IW . . . D 2 1.646 -14.622 -21.633 1 42.68 ? C 0IW 324 A 1 HETATM 3 O O 0IW . . . D 2 2.633 -15.362 -21.657 1 43.38 ? O 0IW 324 A 1 HETATM 4 C C2 0IW . . . D 2 -0.34 -13.636 -22.704 1 40.63 ? C2 0IW 324 A 1 HETATM 5 C C3 0IW . . . D 2 -0.873 -13.473 -24.118 1 39.22 ? C3 0IW 324 A 1 HETATM 6 N N4 0IW . . . D 2 -1.128 -14.802 -24.65 1 38.7 ? N4 0IW 324 A 1 HETATM 7 C CM 0IW . . . D 2 -2.317 -15.037 -25.461 1 37.56 ? CM 0IW 324 A 1 HETATM 8 C C5 0IW . . . D 2 -0.201 -15.902 -24.397 1 39.74 ? C5 0IW 324 A 1 HETATM 9 C C6 0IW . . . D 2 1.109 -15.279 -23.923 1 41.75 ? C6 0IW 324 A 1 HETATM 10 N N 0IW . . . D 2 1.363 -13.918 -20.533 1 42.83 ? N 0IW 324 A 1 HETATM 11 C CA 0IW . . . D 2 2.191 -13.992 -19.327 1 43.77 ? CA 0IW 324 A 1 HETATM 12 C C1 0IW . . . D 2 2.043 -15.348 -18.696 1 44.56 ? C1 0IW 324 A 1 HETATM 13 O O1 0IW . . . D 2 0.937 -15.774 -18.452 1 45.59 ? O1 0IW 324 A 1 HETATM 14 C CB 0IW . . . D 2 1.687 -12.892 -18.381 1 43.92 ? CB 0IW 324 A 1 HETATM 15 C CG 0IW . . . D 2 2.209 -11.538 -18.816 1 43.96 ? CG 0IW 324 A 1 HETATM 16 C CD1 0IW . . . D 2 3.393 -11.036 -18.266 1 44.46 ? CD1 0IW 324 A 1 HETATM 17 C CD2 0IW . . . D 2 1.51 -10.787 -19.76 1 43.21 ? CD2 0IW 324 A 1 HETATM 18 C CE1 0IW . . . D 2 3.867 -9.785 -18.67 1 44.35 ? CE1 0IW 324 A 1 HETATM 19 C CE2 0IW . . . D 2 1.978 -9.537 -20.161 1 43.14 ? CE2 0IW 324 A 1 HETATM 20 C CZ 0IW . . . D 2 3.157 -9.034 -19.612 1 43.59 ? CZ 0IW 324 A 1 HETATM 21 C C11 0IW . . . D 2 5.169 -16.918 -16.309 1 53.47 ? C11 0IW 324 A 1 HETATM 22 C C21 0IW . . . D 2 3.703 -17.315 -16.448 1 48.57 ? C21 0IW 324 A 1 HETATM 23 C C31 0IW . . . D 2 3.1 -17.37 -17.86 1 47.79 ? C31 0IW 324 A 1 HETATM 24 N N2 0IW . . . D 2 3.148 -16.038 -18.448 1 46.15 ? N2 0IW 324 A 1 HETATM 25 C C4 0IW . . . D 2 3.949 -18.251 -18.77 1 47.51 ? C4 0IW 324 A 1 HETATM 26 C C51 0IW . . . D 2 3.403 -18.341 -20.188 1 47.27 ? C51 0IW 324 A 1 HETATM 27 C C1' 0IW . . . D 2 4.091 -19.504 -20.854 1 46.4 ? C1' 0IW 324 A 1 HETATM 28 C C2' 0IW . . . D 2 3.501 -20.774 -20.803 1 45.4 ? C2' 0IW 324 A 1 HETATM 29 C C3' 0IW . . . D 2 4.15 -21.847 -21.402 1 45.85 ? C3' 0IW 324 A 1 HETATM 30 C C4' 0IW . . . D 2 5.365 -21.643 -22.057 1 46.73 ? C4' 0IW 324 A 1 HETATM 31 C C5' 0IW . . . D 2 5.952 -20.373 -22.105 1 46.6 ? C5' 0IW 324 A 1 HETATM 32 C C6' 0IW . . . D 2 5.312 -19.295 -21.497 1 46.09 ? C6' 0IW 324 A 1 HETATM 33 C C12 0IW . . . D 2 6.364 -21.857 -17.697 1 59.38 ? C12 0IW 324 A 1 HETATM 34 C C22 0IW . . . D 2 5.555 -21.769 -16.548 1 59.74 ? C22 0IW 324 A 1 HETATM 35 C C32 0IW . . . D 2 5.446 -20.564 -15.823 1 58.16 ? C32 0IW 324 A 1 HETATM 36 C C41 0IW . . . D 2 6.152 -19.439 -16.25 1 56.66 ? C41 0IW 324 A 1 HETATM 37 S S1 0IW . . . D 2 6.073 -18.049 -15.462 1 57.56 ? S1 0IW 324 A 1 HETATM 38 O O11 0IW . . . D 2 5.553 -18.199 -14.135 1 57.8 ? O11 0IW 324 A 1 HETATM 39 O O2 0IW . . . D 2 7.426 -17.574 -15.33 1 57.44 ? O2 0IW 324 A 1 HETATM 40 C C52 0IW . . . D 2 6.964 -19.538 -17.386 1 57.8 ? C52 0IW 324 A 1 HETATM 41 C C61 0IW . . . D 2 7.079 -20.732 -18.118 1 58.04 ? C61 0IW 324 A 1 # _model_server_stats.io_time_ms 75 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 431 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 41 #